From 58b6ce0ee50d50056bf1aa33f661e7bae1283e64 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 28 Dec 2020 12:28:18 -0600
Subject: [PATCH] Update filenames to new convention
---
workflow/rna-seq.nf | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 402673e..d311523 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -988,7 +988,7 @@ process makeBigWig {
tuple path (bam), path (bai) from dedupBam_makeBigWig
output:
- path ("${repRID}.bw") into bigwig
+ path ("${repRID}_sorted.deduped.bw") into bigwig
script:
"""
@@ -1019,7 +1019,7 @@ process countData {
output:
path ("*_tpmTable.csv") into counts
- path ("*.countData.summary") into countsQC
+ path ("*_countData.summary") into countsQC
path ("assignedReads.csv") into assignedReadsInfer_fl
script:
@@ -1055,11 +1055,11 @@ process countData {
echo -e "LOG: counted" >> ${repRID}.countData.log
# extract assigned reads
- grep -m 1 'Assigned' *.countData.summary | grep -oe '\\([0-9.]*\\)' > assignedReads.csv
+ grep -m 1 'Assigned' *_countData.summary | grep -oe '\\([0-9.]*\\)' > assignedReads.csv
# calculate TPM from the resulting countData table
echo -e "LOG: calculating TPM with R" >> ${repRID}.countData.log
- Rscript calculateTPM.R --count "${repRID}.countData"
+ Rscript calculateTPM.R --count "${repRID}_countData"
# convert gene symbols to Entrez id's
echo -e "LOG: convert gene symbols to Entrez id's" >> ${repRID}.countData.log
@@ -1463,7 +1463,7 @@ process uploadQC {
exist=\$(curl -s https://${source}/ermrest/catalog/2/entity/RNASeq:mRNA_QC/Replicate=${repRID})
if [ "\${exist}" != "[]" ]
then
- rids=\$(echo $exist | grep -o '\\"RID\\":\\".\\{7\\}' | sed 's/^.\\{7\\}//')
+ rids=\$(echo \${exist} | grep -o '\\"RID\\":\\".\\{7\\}' | sed 's/^.\\{7\\}//')
for rid in \${rids}
do
python3 deleteEntry.py -r \${rid} -t mRNA_QC -o ${source} -c \${cookie}
--
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